I recommend buying the 3rd book on this page, Affordable Automation:
http://www.societyofrobots.com/robot_books.shtmlIts usually like ~$10 so worth the money.
I haven't done any multicell work, but everything I've read says each cell should be kept 100% independent from each other. No I/O handshakes, but instead sensors to detect when parts have entered the cell.
This makes early testing and programming simple, so that one cell doesn't affect another. And if one cell fails, the others will just wait.
The additional benefit of error detection is that it allows your factory to run unsupervised at night.